Nematodes are the most abundant metazoans of deep-sea benthic communities, but knowledge of their distribution is limited relative to larger organisms. Whilst some aspects of nematode processing techniques, such as extraction, have been extensively studied, other key elements have attracted little attention. We compared the effect of (1) mesh size (63, 45, and 32 μm) on estimates of nematode abundance, biomass, and body size, and (2) microscope magnification (50 and 100×) on estimates of nematode abundance at bathyal sites (250-3100 m water depth) on the Challenger Plateau and Chatham Rise, south-west Pacific Ocean. Variation in the effectiveness of these techniques was assessed in relation to nematode body size and environmental parameters (water depth, sediment organic matter content, %silt/clay, and chloroplastic pigments). The 63-μm mesh retained a relatively low proportion of total nematode abundance (mean ±SD = 55 ±9%), but most of nematode biomass (90 ± 4%). The proportion of nematode abundance retained on the 45-μm mesh in surface (0-1 cm) and subsurface (1-5 cm) sediment was significantly correlated (P < 0.01) with %silt/clay (R² = 0.39) and chloroplastic pigments (R² = 0.29), respectively. Variation in median nematode body weight showed similar trends, but relationships between mean nematode body weight and environmental parameters were either relatively weak (subsurface sediment) or not significant (surface sediment). Using a low magnification led to significantly lower (on average by 43%) nematode abundance estimates relative to high magnification (P < 0.001), and the magnitude of this difference was significantly correlated (P < 0.05) with total nematode abundance (R²p = 0.53) and the number of small (≤ 250 μm length) individuals (R²p = 0.05). Our results suggest that organic matter input and sediment characteristics influence the abundance of small nematodes in bathyal communities. The abundance of small individuals can, in turn, influence abundance estimates obtained using different mesh sizes and microscope magnifications.